bio test #4 - enzymes

what is cellular metabolism

sum of all chemical reactions of the cell

what are the two significant parts of cellular metabolism

catabolism, anabolism

what does catabolism refer to

reactions that break down large molecules (reactants) into smaller molecules (products)

what does anabolism refer to

reactions that make large molecules (products) from smaller molecules (reactants

how do we know if a reaction will proceed in the indicated direction?

use the concept of free energy

what is free energy and what does /\G delta G represent

amount of energy available after a chemical reaction has occurred. represents the change in free energy of a reaction

how is the change in free energy calculated

free energy of products - free energy of reactants

what happens if there is negative /\G? (-/\G)

products have less free energy than reactants and the reaction will occur in the direction indicated

what are exergonic reactions (-/\G)

spontaneous and release energy

what are endergonic reactions (+/\G)

require an input of energy

how does the body use endergonic and exergonic reactions?

many reactions like protein synthesis are endergonic and use energy from exergonic reactions

ATP is a carrier of what?

energy between exergonic and endergonic reactions

why is the amount of ATP minimal

it is constantly being made from ADP and a molecule of inorganic phosphate

what percent of free energy of glucose is transformed into ATP? why?

39 because the rest is lost as heat

how does the endergonic reaction occur with ATP

ATP is made from ADP and inorganic phosphorus which requires an input of energy from other sources like cellular respiration

how does the exergonic reaction occur with ATP

hydrolysis of ATP releases previously stored energy. the change in free energy is used for endergonic reactions in the cell

what are three processes that are driven by the energy released by the exergonic reaction of ATP

protein synthesis, nerve conduction, muscle contraction

how are chemical reactions in the cell linked

by metabolic pathways

what are the two types of pathways in a metabolic pathway

linear with a final product or cyclical where the reactant is regenerated

what are enzymes

proteins that function as catalysts to speed a chemical reaction

what is a form of a RNA molecule that acts as a catalyst

ribozymes

what do catalysts do

they participate in chemical reactions but are not used up by the reaction, they increase the rate of reaction

what are the reactants called in an enzymatic reaction

enzyme substrates

in this metabolic pathway, B is the substrate for what?

enzyme 2

what is energy of activation (E_a)

energy that must be added for molecules to react with one another even if /\G is negative

what do enzymes do in terms of energy of activation

they speed up the rate of reaction by lowering the activation energy

what is the equation that shows what happens when an enzyme forms a complex with its substrate

substrate + enzyme → enzyme-substrate complex→ enzyme + product

what part of the enzyme complexes with the substrate(s) and to form what?

one small part called the active site complexes with the substrate to form an enzyme-substrate complex. they fit together in such a way that the substrates can react

what is the induced fit model

the active site on an enzyme that undergoes a slight change for the substrates

what two processes can an enzymatic reaction result in

degradation of a substrate into multiple products (catabolism) or the synthesis of a product form multiple substrates (anabolism)

after the reaction has been completed, what occurs?

the products are released and the active site returns to its original shape, ready to bind to another substrate molecule

some enzymes do more than simply complex with their substrate(s) and instead participate in the reaction, give me an example of this

trypsin digests protein by breaking peptide bonds when the active site interacts with the peptide bond to break the bond and then introduce components of water

because enzymes bind only with their substrates, what is the enzyme for the lipid substrate

lipase

because enzymes bind only with their substrates, what is the enzyme for the starch substrate

amylase

because enzymes bind only with their substrates, what is the enzyme for the maltose substrate

maltase

because enzymes bind only with their substrates, what is the enzyme for the ribonucleic acid substrate

ribonuclease

because enzymes bind only with their substrates, what is the enzyme for the lactose substrate

lactase

what are factors that can affect the rate of an enzymatic reaction

the amount of substrate present for the reaction, environmental conditions like temperature and pH, enzyme activation, enzyme inhibition, and the presence of cofactors

generally, what happens to enzyme activity when substrate concentration increases why? (2)

enzyme activity increases because there are more collisions between the enzyme and substrate molecules and because there are more substrate molecules available to fill more active sites which means more products can result per unit time

with substrate concentration, why does a maximum rate exist?

once all active sites on an enzyme are filled with substrate, the reaction cannot go any faster

what happens to enzyme activity when temperature increases

enzyme activity increases because there are more effective collisions between enzyme and substrate

what happens to enzymes if the temperature rises beyond a certain point

it becomes inactive because it is denatured

what happens when an enzyme becomes denatured

the enzyme changes shape from the loss of secondary and tertiary structure and can no longer bind its substrates

do all enzymes have the same pH that they prefer?

no, each enzyme has a unique pH at which the rate of the reaction is highest

what happens to enzymes like pepsin and trypsin at their preferred pH

they have their normal shape and function properly

what maintains an enzymes structure?

interactions between R groups like hydrogen bonds

what does a change in pH do to an enzyme?

it can change the ionization of R groups and disrupts interactions which can change the enzymes shape

when does extreme pH changes cause?

denaturation which leads to an enzyme being unable to combine efficiently with its substrate

are enzymes always needed in a cell?

no, cells only produce them when needed

how can a cell increase enzyme concentration or decrease enzyme concentration?

by turning genes on or off

can enzymes exist in an inactive form

yes, enzymes can be present but inactive

what is enzyme activation?

turning an inactive enzyme into an active one

what are different ways that enzymes can be activated

interaction with another protein or molecule, removal of part of the protein, addition or removal of one or more phosphate groups

how are enzymes activated by phosphate groups

by adding or removing phosphate groups

what does kinase do vs phosphatase

kinase adds phosphate groups while phosphatase removes them

what controls enzyme activity in cells

signals like messengers and hormones

when does enzyme inhibition occur

when the substrate is unable to bind to the active site of an enzyme

does enzyme inhibition increase or decrease enzyme activity

decreases because substrates can’t bind to the active site

what is an important type on inhibition

feedback inhibition

what is feedback inhibition

when a product of a reaction stops the enzyme from working

what happens when there is a lot of product in feedback inhibition

the product binds to the enzyme and prevents the substrate from binding

what happens when the product is used up?

inhibition decreases and the enzyme can work again

why is feedback inhibition important

it keeps product levels within a certain range

what happens in more complex feedback inhibition

the end product binds somewhere other than the active site which can change the shape of the active site and the substrate cannot bind

what happens to the metabolic pathway when inhibited

it shuts down and no more product is made

what is a common example of enzyme inhibitors

poisons like cyanide and penicillin

what does cyanide do?

has a lethal affect on us as it acts as an inhibitor for an enzyme needed for cellular respiration in all cells

what does penicillin do? (affects bacteria not humans)

antimicrobial agent that blocks the active sites of an enzyme used to construct a molecule of the cell walls of bacteria

most enzymes require what to function properly

inorganic ions or organic non-protein molecule

what are these inorganic ions known as?

cofactors like copper, zinc, or iron

what are the organic, nonprotein molecules called?

coenzymes that assist the enzyme by accepting or contributing atoms to the reaction

how do we obtain coenzymes

by eating plants or animals that have eaten plants

what are vitamins (component of coenzymes)

small organic molecules that we need in our diet for the synthesis of coenzymes

how is a vitamin a component of a coenzyme

the vitamin becomes a part of the coenzymes molecular structure

what coenzyme is niacin a part of? how about riboflavin (B₂)?

NAD, FAD

what does a deficiency of vitamins cause?

a lack of the coenzyme and therefore a lack of certain enzymatic actions

in humans, when we don’t get enough vitamins what are examples of vitamin-deficiency symptoms

a skin disease called pellagra from niacin deficiency and cracks at the corners of the mouth from riboflavin deficiency